Your message dated Fri, 23 Sep 2011 03:02:31 +0000
with message-id <[email protected]>
and subject line Bug#638953: fixed in nipype 0.4.1-2
has caused the Debian Bug report #638953,
regarding nipype: FTBFS: ImportError: No module named design_matrix
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
638953: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=638953
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: nipype
Version: 0.4.1-1
Severity: serious
Justification: fails to build from source
nipype FTBFS in unstable:
| python ../tools/ex2rst \
| --project Nipype \
| --outdir
/build/nipype-rFhixh/nipype-0.4.1/doc/users/examples \
| ../examples/freesurfer_tutorial.py \
| ../examples/fsl_tutorial2.py \
| ../examples/fsl_feeds_tutorial.py \
| ../examples/spm_tutorial.py \
| ../examples/spm_face_tutorial.py \
| ../examples/spm_auditory_tutorial.py \
| ../examples/fsl_dti_tutorial.py \
| ../examples/camino_dti_tutorial.py \
| ../examples/connectivity_tutorial.py \
| ../examples/dtk_dti_tutorial.py \
| ../examples/dtk_odf_tutorial.py \
| ../examples/spm_tutorial2.py \
| ../examples/spm_dartel_tutorial.py \
| ../examples/dartmouth_workshop_2010.py \
| ../examples/nipy_tutorial.py
| examples2rst finished.
| rm -rf api/generated
| #python ../tools/build_modref_templates.py
| rm -rf interfaces/generated
| python ../tools/build_interface_docs.py
| /usr/lib/pymodules/python2.6/matplotlib/__init__.py:890: UserWarning: This
call to matplotlib.use() has no effect
| because the the backend has already been chosen;
| matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
| or matplotlib.backends is imported for the first time.
|
| if warn: warnings.warn(_use_error_msg)
| WARNING: Empty - nipype
| WARNING: Empty - nipype.algorithms
| CreateNifti
| Generating inputs/outputs doc for: nipype.algorithms.misc CreateNifti
| Distance
| Generating inputs/outputs doc for: nipype.algorithms.misc Distance
| ModifyAffine
| Generating inputs/outputs doc for: nipype.algorithms.misc ModifyAffine
| Overlap
| Generating inputs/outputs doc for: nipype.algorithms.misc Overlap
| PickAtlas
| Generating inputs/outputs doc for: nipype.algorithms.misc PickAtlas
| SimpleThreshold
| Generating inputs/outputs doc for: nipype.algorithms.misc SimpleThreshold
| TSNR
| Generating inputs/outputs doc for: nipype.algorithms.misc TSNR
| >>> DEBIAN doc building with missing externals >>>: gcd() takes exactly 2
arguments (0 given)
| >>> DEBIAN doc building with missing externals >>>: gen_info() takes exactly
1 argument (0 given)
| >>> DEBIAN doc building with missing externals >>>: orth() takes exactly 2
arguments (0 given)
| >>> DEBIAN doc building with missing externals >>>: scale_timings() takes
exactly 4 arguments (0 given)
| >>> DEBIAN doc building with missing externals >>>: spm_hrf() takes at least
1 argument (0 given)
| SpecifyModel
| Generating inputs/outputs doc for: nipype.algorithms.modelgen SpecifyModel
| SpecifySPMModel
| Generating inputs/outputs doc for: nipype.algorithms.modelgen SpecifySPMModel
| SpecifySparseModel
| Generating inputs/outputs doc for: nipype.algorithms.modelgen
SpecifySparseModel
| SpecifySparseSPMModel
| 'SpecifySparseSPMModel'
| ArtifactDetect
| Generating inputs/outputs doc for: nipype.algorithms.rapidart ArtifactDetect
| StimulusCorrelation
| Generating inputs/outputs doc for: nipype.algorithms.rapidart
StimulusCorrelation
| WARNING: Empty - nipype.interfaces
| WARNING: Empty - nipype.interfaces.afni
| WARNING: Empty - nipype.interfaces.afni.base
| WARNING: Empty - nipype.interfaces.afni.preprocess
| camino setup test
| camino teardown test
| WARNING: Empty - nipype.interfaces.camino
| Conmap
| Generating inputs/outputs doc for: nipype.interfaces.camino.connectivity
Conmap
| AnalyzeHeader
| Generating inputs/outputs doc for: nipype.interfaces.camino.convert
AnalyzeHeader
| DT2NIfTI
| Generating inputs/outputs doc for: nipype.interfaces.camino.convert DT2NIfTI
| Image2Voxel
| Generating inputs/outputs doc for: nipype.interfaces.camino.convert
Image2Voxel
| NIfTIDT2Camino
| Generating inputs/outputs doc for: nipype.interfaces.camino.convert
NIfTIDT2Camino
| ProcStreamlines
| Generating inputs/outputs doc for: nipype.interfaces.camino.convert
ProcStreamlines
| TractShredder
| Generating inputs/outputs doc for: nipype.interfaces.camino.convert
TractShredder
| VtkStreamlines
| Generating inputs/outputs doc for: nipype.interfaces.camino.convert
VtkStreamlines
| ComputeEigensystem
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti
ComputeEigensystem
| ComputeFractionalAnisotropy
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti
ComputeFractionalAnisotropy
| ComputeMeanDiffusivity
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti
ComputeMeanDiffusivity
| ComputeTensorTrace
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti
ComputeTensorTrace
| DTIFit
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti DTIFit
| DTLUTGen
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti DTLUTGen
| ModelFit
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti ModelFit
| PicoPDFs
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti PicoPDFs
| Track
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti Track
| TrackBallStick
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackBallStick
| TrackBayesDirac
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti
TrackBayesDirac
| TrackBootstrap
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackBootstrap
| TrackDT
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackDT
| TrackPICo
| Generating inputs/outputs doc for: nipype.interfaces.camino.dti TrackPICo
| camino2trackvis setup test
| camino2trackvis teardown test
| WARNING: Empty - nipype.interfaces.camino2trackvis
| Camino2Trackvis
| Generating inputs/outputs doc for: nipype.interfaces.camino2trackvis.convert
Camino2Trackvis
| Trackvis2Camino
| Generating inputs/outputs doc for: nipype.interfaces.camino2trackvis.convert
Trackvis2Camino
| WARNING: Empty - nipype.interfaces.cmtk
| >>> DEBIAN doc building with missing externals >>>: cmat() takes exactly 7
arguments (0 given)
| >>> DEBIAN doc building with missing externals >>>: create_endpoints_array()
takes exactly 2 arguments (0 given)
| >>> DEBIAN doc building with missing externals >>>: length() takes at least
1 argument (0 given)
| >>> DEBIAN doc building with missing externals >>>: save_fibers() takes
exactly 4 arguments (0 given)
| CreateMatrix
| Generating inputs/outputs doc for: nipype.interfaces.cmtk.cmtk CreateMatrix
| ROIGen
| Generating inputs/outputs doc for: nipype.interfaces.cmtk.cmtk ROIGen
| CFFConverter
| Generating inputs/outputs doc for: nipype.interfaces.cmtk.convert CFFConverter
| MergeCNetworks
| Generating inputs/outputs doc for: nipype.interfaces.cmtk.convert
MergeCNetworks
| Dcm2nii
| Generating inputs/outputs doc for: nipype.interfaces.dcm2nii Dcm2nii
| WARNING: Empty - nipype.interfaces.diffusion_toolkit
| Info
| Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.base
Info
| DTIRecon
| Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.dti
DTIRecon
| DTITracker
| Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.dti
DTITracker
| HARDIMat
| Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.odf
HARDIMat
| ODFRecon
| Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.odf
ODFRecon
| ODFTracker
| Generating inputs/outputs doc for: nipype.interfaces.diffusion_toolkit.odf
ODFTracker
| SplineFilter
| Generating inputs/outputs doc for:
nipype.interfaces.diffusion_toolkit.postproc SplineFilter
| WARNING: Empty - nipype.interfaces.freesurfer
| Info
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.base Info
| Binarize
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model Binarize
| Concatenate
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model
Concatenate
| GLMFit
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model GLMFit
| Label2Vol
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model
Label2Vol
| MRISPreproc
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model
MRISPreproc
| OneSampleTTest
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model
OneSampleTTest
| SegStats
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.model SegStats
| ApplyVolTransform
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
ApplyVolTransform
| BBRegister
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
BBRegister
| DICOMConvert
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
DICOMConvert
| FitMSParams
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
FitMSParams
| MRIConvert
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
MRIConvert
| ParseDICOMDir
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
ParseDICOMDir
| ReconAll
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
ReconAll
| Resample
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
Resample
| RobustRegister
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
RobustRegister
| Smooth
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
Smooth
| SynthesizeFLASH
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
SynthesizeFLASH
| UnpackSDICOMDir
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.preprocess
UnpackSDICOMDir
| ApplyMask
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils
ApplyMask
| ImageInfo
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils
ImageInfo
| MRIsConvert
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils
MRIsConvert
| SampleToSurface
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils
SampleToSurface
| SurfaceSmooth
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils
SurfaceSmooth
| SurfaceSnapshots
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils
SurfaceSnapshots
| SurfaceTransform
| Generating inputs/outputs doc for: nipype.interfaces.freesurfer.utils
SurfaceTransform
| test setup
| >>> DEBIAN doc building with missing externals >>>:
| test teardown
| WARNING: Empty - nipype.interfaces.fsl
| Info
| Generating inputs/outputs doc for: nipype.interfaces.fsl.base Info
| BEDPOSTX
| FSL environment variables not set
| DTIFit
| FSL environment variables not set
| DistanceMap
| FSL environment variables not set
| EddyCorrect
| FSL environment variables not set
| FindTheBiggest
| FSL environment variables not set
| MakeDyadicVectors
| FSL environment variables not set
| ProbTrackX
| FSL environment variables not set
| ProjThresh
| FSL environment variables not set
| TractSkeleton
| FSL environment variables not set
| VecReg
| FSL environment variables not set
| XFibres
| FSL environment variables not set
| ApplyMask
| FSL environment variables not set
| ApplyMaskInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths ApplyMaskInput
| BinaryMaths
| FSL environment variables not set
| BinaryMathsInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths
BinaryMathsInput
| ChangeDataType
| FSL environment variables not set
| ChangeDataTypeInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths
ChangeDataTypeInput
| DilateImage
| FSL environment variables not set
| DilateInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths DilateInput
| ErodeImage
| FSL environment variables not set
| ErodeInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths ErodeInput
| IsotropicSmooth
| FSL environment variables not set
| IsotropicSmoothInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths
IsotropicSmoothInput
| KernelInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths KernelInput
| MathsCommand
| FSL environment variables not set
| MathsInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths MathsInput
| MathsOutput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths MathsOutput
| MeanImage
| FSL environment variables not set
| MeanImageInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths MeanImageInput
| MultiImageMaths
| FSL environment variables not set
| MultiImageMathsInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths
MultiImageMathsInput
| SpatialFilter
| FSL environment variables not set
| SpatialFilterInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths
SpatialFilterInput
| TemporalFilter
| FSL environment variables not set
| TemporalFilterInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths
TemporalFilterInput
| Threshold
| FSL environment variables not set
| UnaryMaths
| FSL environment variables not set
| UnaryMathsInput
| Generating inputs/outputs doc for: nipype.interfaces.fsl.maths UnaryMathsInput
| Cluster
| FSL environment variables not set
| ContrastMgr
| FSL environment variables not set
| FEAT
| FSL environment variables not set
| FEATModel
| FSL environment variables not set
| FEATRegister
| Generating inputs/outputs doc for: nipype.interfaces.fsl.model FEATRegister
| FILMGLS
| FSL environment variables not set
| FLAMEO
| FSL environment variables not set
| L2Model
| Generating inputs/outputs doc for: nipype.interfaces.fsl.model L2Model
| Level1Design
| Generating inputs/outputs doc for: nipype.interfaces.fsl.model Level1Design
| MELODIC
| FSL environment variables not set
| MultipleRegressDesign
| Generating inputs/outputs doc for: nipype.interfaces.fsl.model
MultipleRegressDesign
| Randomise
| FSL environment variables not set
| SMM
| FSL environment variables not set
| SmoothEstimate
| FSL environment variables not set
| ApplyWarp
| FSL environment variables not set
| ApplyXfm
| FSL environment variables not set
| BET
| FSL environment variables not set
| FAST
| FSL environment variables not set
| FLIRT
| FSL environment variables not set
| FNIRT
| FSL environment variables not set
| FUGUE
| FSL environment variables not set
| MCFLIRT
| FSL environment variables not set
| PRELUDE
| FSL environment variables not set
| SUSAN
| Traceback (most recent call last):
| File "../tools/build_interface_docs.py", line 49, in <module>
| FSL environment variables not set
| SliceTimer
| FSL environment variables not set
| ConvertXFM
| FSL environment variables not set
| ExtractROI
| docwriter.write_api_docs(outdir)
| FSL environment variables not set
| File "/build/nipype-rFhixh/nipype-0.4.1/tools/interfacedocgen.py", line
556, in write_api_docs
| FilterRegressor
| FSL environment variables not set
| ImageMaths
| FSL environment variables not set
| ImageMeants
| FSL environment variables not set
| ImageStats
| FSL environment variables not set
| Merge
| FSL environment variables not set
| Overlay
| FSL environment variables not set
| PlotMotionParams
| FSL environment variables not set
| PlotTimeSeries
| FSL environment variables not set
| PowerSpectrum
| FSL environment variables not set
| Slicer
| self.write_modules_api(modules,outdir)
| FSL environment variables not set
| File "/build/nipype-rFhixh/nipype-0.4.1/tools/interfacedocgen.py", line
523, in write_modules_api
| Smooth
| FSL environment variables not set
| Split
| FSL environment variables not set
| SwapDimensions
| FSL environment variables not set
| >>> DEBIAN doc building with missing externals >>>: add_traits() takes at
least 2 arguments (0 given)
| >>> DEBIAN doc building with missing externals >>>: copytree() takes exactly
2 arguments (0 given)
| >>> DEBIAN doc building with missing externals >>>: push_file() takes
exactly 5 arguments (0 given)
| >>> DEBIAN doc building with missing externals >>>: quote_id() takes exactly
1 argument (0 given)
| >>> DEBIAN doc building with missing externals >>>: unquote_id() takes
exactly 1 argument (0 given)
| DataGrabber
| Generating inputs/outputs doc for: nipype.interfaces.io DataGrabber
| DataSink
| Generating inputs/outputs doc for: nipype.interfaces.io DataSink
| FreeSurferSource
| api_str = self.generate_api_doc(m)
| Generating inputs/outputs doc for: nipype.interfaces.io FreeSurferSource
| IOBase
| File "/build/nipype-rFhixh/nipype-0.4.1/tools/interfacedocgen.py", line
312, in generate_api_doc
| Generating inputs/outputs doc for: nipype.interfaces.io IOBase
| SQLiteSink
| __init__() takes exactly 2 arguments (1 given)
| XNATSink
| Generating inputs/outputs doc for: nipype.interfaces.io XNATSink
| XNATSource
| Generating inputs/outputs doc for: nipype.interfaces.io XNATSource
| WARNING: Empty - nipype.interfaces.nipy
| __import__(uri)
| File "/build/nipype-rFhixh/nipype-0.4.1/nipype/interfaces/nipy/__init__.py", line
1, in <module>
| from model import FitGLM, EstimateContrast
| File "/build/nipype-rFhixh/nipype-0.4.1/nipype/interfaces/nipy/model.py", line 9,
in <module>
| import nipy.labs.utils.design_matrix as dm
| ImportError: No module named design_matrix
| make[1]: *** [api] Error 1
-- System Information:
Debian Release: wheezy/sid
APT prefers unstable
APT policy: (990, 'unstable'), (500, 'experimental')
Architecture: i386 (x86_64)
--
Jakub Wilk
--- End Message ---
--- Begin Message ---
Source: nipype
Source-Version: 0.4.1-2
We believe that the bug you reported is fixed in the latest version of
nipype, which is due to be installed in the Debian FTP archive:
nipype_0.4.1-2.debian.tar.gz
to main/n/nipype/nipype_0.4.1-2.debian.tar.gz
nipype_0.4.1-2.dsc
to main/n/nipype/nipype_0.4.1-2.dsc
python-nipype-doc_0.4.1-2_all.deb
to main/n/nipype/python-nipype-doc_0.4.1-2_all.deb
python-nipype_0.4.1-2_all.deb
to main/n/nipype/python-nipype_0.4.1-2_all.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Yaroslav Halchenko <[email protected]> (supplier of updated nipype package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Thu, 22 Sep 2011 14:20:05 -0400
Source: nipype
Binary: python-nipype python-nipype-doc
Architecture: source all
Version: 0.4.1-2
Distribution: unstable
Urgency: low
Maintainer: NeuroDebian Team <[email protected]>
Changed-By: Yaroslav Halchenko <[email protected]>
Description:
python-nipype - Neuroimaging data analysis pipelines in Python
python-nipype-doc - Neuroimaging data analysis pipelines in Python --
documentation
Closes: 638953
Changes:
nipype (0.4.1-2) unstable; urgency=low
.
* Cherry-picked post-release nipy-compatibility patch
up_recent_nipy_reference (Closes: #638953). Thanks Barry for the reminder.
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--- End Message ---
